The problem was that components of Flame were signed using a forged certificate that the attacker were able to create by exploiting a weakness in Microsoft Terminal Services, how allow users to sign code with Microsoft certificates.

Microsoft has issue a security advisory (MSA-2718704) and an update (KB-2718704) how will remove the untrusted certificates.

But since today, “Microsoft Root Certificate Authority” root certificate, “Microsoft Update Secure Server CA 1” intermediate certificate are not more trusted by majority of Internet browsers like Firefox, Chrome, Safari and Opera. The cause is that Microsoft has regenerate the Windows Update certificate chain. The chain of trust is broken (Qualys SSL Labs – SSL Shopper SSL Checker) for www.update.microsoft.com and update.microsoft.com.